Spruce giga-genomes: structurally similar yet distinctive with differentially expanding gene families and rapidly evolving genes.

Spruces (Picea spp.) are coniferous trees widespread in boreal and mountainous forests of the northern hemisphere, with large economic significance and enormous contributions to global carbon sequestration. Spruces harbor very large genomes with high repetitiveness, hampering their comparative analysis. Here, we present and compare the genomes of four different North American spruces: the genome assemblies for Engelmann spruce (Picea engelmannii) and Sitka spruce (Picea sitchensis) together with improved and more contiguous genome assemblies for white spruce (Picea glauca) and for a naturally occurring introgress of these three species known as interior spruce (P. engelmannii × glauca × sitchensis). The genomes were structurally similar, and a large part of scaffolds could be anchored to a genetic map. The composition of the interior spruce genome indicated asymmetric contributions from the three ancestral genomes. Phylogenetic analysis of the nuclear and organelle genomes revealed a topology indicative of ancient reticulation. Different patterns of expansion of gene families among genomes were observed and related with presumed diversifying ecological adaptations. We identified rapidly evolving genes that harbored high rates of non-synonymous polymorphisms relative to synonymous ones, indicative of positive selection and its hitchhiking effects. These gene sets were mostly distinct between the genomes of ecologically contrasted species, and signatures of convergent balancing selection were detected. Stress and stimulus response was identified as the most frequent function assigned to expanding gene families and rapidly evolving genes. These two aspects of genomic evolution were complementary in their contribution to divergent evolution of presumed adaptive nature. These more contiguous spruce giga-genome sequences should strengthen our understanding of conifer genome structure and evolution, as their comparison offers clues into the genetic basis of adaptation and ecology of conifers at the genomic level. They will also provide tools to better monitor natural genetic diversity and improve the management of conifer forests. The genomes of four closely related North American spruces indicate that their high similarity at the morphological level is paralleled by the high conservation of their physical genome structure. Yet, the evidence of divergent evolution is apparent in their rapidly evolving genomes, supported by differential expansion of key gene families and large sets of genes under positive selection, largely in relation to stimulus and environmental stress response.

Remediation of Thirdhand Tobacco Smoke with Ozone: Probing Deep Reservoirs in Carpets.

We assessed the efficacy of ozonation as an indoor remediation strategy by evaluating how a carpet serves as a sink and long-term source of thirdhand tobacco smoke (THS) while protecting contaminants absorbed in deep reservoirs by scavenging ozone. Specimens from unused carpet that was exposed to smoke in the lab ("fresh THS") and contaminated carpets retrieved from smokers' homes ("aged THS") were treated with 1000 ppb ozone in bench-scale tests. Nicotine was partially removed from fresh THS specimens by volatilization and oxidation, but it was not significantly eliminated from aged THS samples. By contrast, most of the 24 polycyclic aromatic hydrocarbons detected in both samples were partially removed by ozone. One of the home-aged carpets was installed in an 18 m3 room-sized chamber, where its nicotine emission rate was 950 ng day-1 m-2. In a typical home, such daily emissions could amount to a non-negligible fraction of the nicotine released by smoking one cigarette. The operation of a commercial ozone generator for a total duration of 156 min, reaching concentrations up to 10,000 ppb, did not significantly reduce the carpet nicotine loading (26-122 mg m-2). Ozone reacted primarily with carpet fibers, rather than with THS, leading to short-term emissions of aldehydes and aerosol particles. Hence, by being absorbed deeply into carpet fibers, THS constituents can be partially shielded from ozonation.

Associations between prenatal and early-life air pollution exposure and lung function in young children: Exploring influential windows of exposure on lung development.

BACKGROUND: Evidence in the literature suggests that air pollution exposures experienced prenatally and early in life can be detrimental to normal lung development, however the specific timing of critical windows during development is not fully understood. OBJECTIVES: We evaluated air pollution exposures during the prenatal and early-life period in association with lung function at ages 6-9, in an effort to identify potentially influential windows of exposure for lung development. METHODS: Our study population consisted of 222 children aged 6-9 from the Fresno-Clovis metro area in California with spirometry data collected between May 2015 and May 2017. We used distributed-lag non-linear models to flexibly model the exposure-lag-response for monthly average exposure to fine particulate matter (PM2.5) and ozone (O3) during the prenatal months and first three years of life in association with forced vital capacity (FVC), and forced expiratory volume in the first second (FEV1), adjusted for covariates. RESULTS: PM2.5 exposure during the prenatal period and the first 3-years of life was associated with lower FVC and FEV1 assessed at ages 6-9. Specifically, an increase from the 5th percentile of the observed monthly average exposure (7.55 µg/m3) to the median observed exposure (12.69 µg/m3) for the duration of the window was associated with 0.42 L lower FVC (95% confidence interval (CI): -0.82, -0.03) and 0.38 L lower FEV1 (95% CI: -0.75, -0.02). The shape of the lag-response indicated that the second half of pregnancy may be a particularly influential window of exposure. Associations for ozone were not as strong and typically CIs included the null. CONCLUSIONS: Our findings indicate that prenatal and early-life exposures to PM2.5 are associated with decreased lung function later in childhood. Exposures during the latter months of pregnancy may be especially influential.

AMPlify: attentive deep learning model for discovery of novel antimicrobial peptides effective against WHO priority pathogens.

BACKGROUND: Antibiotic resistance is a growing global health concern prompting researchers to seek alternatives to conventional antibiotics. Antimicrobial peptides (AMPs) are attracting attention again as therapeutic agents with promising utility in this domain, and using in silico methods to discover novel AMPs is a strategy that is gaining interest. Such methods can sift through large volumes of candidate sequences and reduce lab screening costs. RESULTS: Here we introduce AMPlify, an attentive deep learning model for AMP prediction, and demonstrate its utility in prioritizing peptide sequences derived from the Rana [Lithobates] catesbeiana (bullfrog) genome. We tested the bioactivity of our predicted peptides against a panel of bacterial species, including representatives from the World Health Organization's priority pathogens list. Four of our novel AMPs were active against multiple species of bacteria, including a multi-drug resistant isolate of carbapenemase-producing Escherichia coli. CONCLUSIONS: We demonstrate the utility of deep learning based tools like AMPlify in our fight against antibiotic resistance. We expect such tools to play a significant role in discovering novel candidates of peptide-based alternatives to classical antibiotics.

Autoimmunity to a ribonucleoprotein drives neuron loss in multiple sclerosis models.

Neurodegeneration, the progressive loss or damage to neurons and axons, underlies permanent disability in multiple sclerosis (MS); yet its mechanisms are incompletely understood. Recent data indicates autoimmunity to several intraneuronal antigens, including the RNA binding protein (RBP) heterogenous nuclear ribonucleoprotein A1 (hnRNP A1), as contributors to neurodegeneration. We previously showed that addition of anti-hnRNP A1 antibodies, which target the same immunodominant domain of MS IgG, to mice with experimental autoimmune encephalomyelitis (EAE) worsened disease and resulted in an exacerbation of hnRNP A1 dysfunction including cytoplasmic mislocalization of hnRNP A1, stress granule (SG) formation and neurodegeneration in the chronic stages of disease. Because this previous study focused on a singular timepoint during EAE, it is unclear whether anti-hnRNP A1 antibody induced hnRNP A1 dysfunction caused neurodegeneration or was result of it. In the present study, we analyzed in vivo and in vitro models of anti-hnRNP A1 antibody-mediated autoimmunity for markers of hnRNP A1 dysfunction and neurodegeneration over a time course to gain a better understanding of the connection between hnRNP A1 dysfunction and neurodegeneration. Anti-hnRNP A1 antibody treatment resulted in increased neuronal hnRNP A1 mislocalization and nuclear depletion temporally followed by altered RNA expression and SG formation, and lastly an increase in necroptotic signalling and neuronal cell death. Treatment with necrostatin-1s inhibited necroptosis and partially rescued anti-hnRNP A1 antibody-mediated neurodegeneration while clathrin knockdown specifically inhibited anti-hnRNP A1 antibody uptake into neurons. This data identifies a novel antibody-mediated mechanism of neurodegeneration, which may be targeted to inhibit neurodegeneration and prevent permanent neurological decline in persons living with MS.

End-stage renal disease and metalworking fluid exposure.

OBJECTIVE: Despite increasing prevalence of end-stage renal disease (ESRD), little attention has been directed to how occupational exposures may contribute to risk. Our objective was to investigate the relationship between metalworking fluids (MWF) and ESRD in a cohort of 36 703 male autoworkers. METHODS: We accounted for competing risk of death, using the subdistribution hazard approach to estimate subhazard ratios (sHRs) and 95% CIs in models with cubic splines for cumulative exposure to MWF (straight, soluble or synthetic). RESULTS: Based on 501 ESRD cases and 13 434 deaths, we did not observe an association between MWF and ESRD overall. We observed modest associations between MWF and ESRD classification of glomerulonephritis and diabetic nephropathy. For glomerulonephritis, the 60th percentile of straight MWF was associated with an 18% increased subhazard (sHR=1.18, 95% CI: 0.99 to 1.41). For diabetic nephropathy, the subhazard increased 28% at the 60th percentile of soluble MWF (sHR=1.28, 95% CI: 1.00 to 1.64). Differences by race suggest that black males may have higher disease rates following MWF exposure. CONCLUSIONS: Exposure to straight and soluble MWF may be related to ESRD classification, though this relationship should be further examined.

Traffic-related air pollution is associated with glucose dysregulation, blood pressure, and oxidative stress in children.

BACKGROUND: Metabolic syndrome increases the risk of cardiovascular disease in adults. Antecedents likely begin in childhood and whether childhood exposure to air pollution plays a contributory role is not well understood. OBJECTIVES: To assess whether children's exposure to air pollution is associated with markers of risk for metabolic syndrome and oxidative stress, a hypothesized mediator of air pollution-related health effects. METHODS: We studied 299 children (ages 6-8) living in the Fresno, CA area. At a study center visit, questionnaire and biomarker data were collected. Outcomes included hemoglobin A1c (HbA1c), urinary 8-isoprostane, systolic blood pressure (SBP), and BMI. Individual-level exposure estimates for a set of four pollutants that are constituents of traffic-related air pollution (TRAP) - the sum of 4-, 5-, and 6-ring polycyclic aromatic hydrocarbon compounds (PAH456), NO2, elemental carbon, and fine particulate matter (PM2.5) - were modeled at the primary residential location for 1-day lag, and 1-week, 1-month, 3-month, 6-month, and 1-year averages prior to each participant's visit date. Generalized additive models were used to estimate associations between each air pollutant exposure and outcome. RESULTS: The study population was 53% male, 80% Latinx, 11% Black and largely low-income (6% were White and 3% were Asian/Pacific Islander). HbA1c percentage was associated with longer-term increases in TRAP; for example a 4.42 ng/m3 increase in 6-month average PAH456 was associated with a 0.07% increase (95% CI: 0.01, 0.14) and a 3.62 µg/m3 increase in 6-month average PM2.5 was associated with a 0.06% increase (95% CI: 0.01, 0.10). The influence of air pollutants on blood pressure was strongest at 3 months; for example, a 6.2 ppb increase in 3-month average NO2 was associated with a 9.4 mmHg increase in SBP (95% CI: 2.8, 15.9). TRAP concentrations were not significantly associated with anthropometric or adipokine measures. Short-term TRAP exposure averages were significantly associated with creatinine-adjusted urinary 8-isoprostane. DISCUSSION: Our results suggest that both short- and longer-term estimated individual-level outdoor residential exposures to several traffic-related air pollutants, including ambient PAHs, are associated with biomarkers of risk for metabolic syndrome and oxidative stress in children.

ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter.

The assembly of DNA sequences de novo is fundamental to genomics research. It is the first of many steps toward elucidating and characterizing whole genomes. Downstream applications, including analysis of genomic variation between species, between or within individuals critically depend on robustly assembled sequences. In the span of a single decade, the sequence throughput of leading DNA sequencing instruments has increased drastically, and coupled with established and planned large-scale, personalized medicine initiatives to sequence genomes in the thousands and even millions, the development of efficient, scalable and accurate bioinformatics tools for producing high-quality reference draft genomes is timely. With ABySS 1.0, we originally showed that assembling the human genome using short 50-bp sequencing reads was possible by aggregating the half terabyte of compute memory needed over several computers using a standardized message-passing system (MPI). We present here its redesign, which departs from MPI and instead implements algorithms that employ a Bloom filter, a probabilistic data structure, to represent a de Bruijn graph and reduce memory requirements. We benchmarked ABySS 2.0 human genome assembly using a Genome in a Bottle data set of 250-bp Illumina paired-end and 6-kbp mate-pair libraries from a single individual. Our assembly yielded a NG50 (NGA50) scaffold contiguity of 3.5 (3.0) Mbp using <35 GB of RAM. This is a modest memory requirement by today's standards and is often available on a single computer. We also investigate the use of BioNano Genomics and 10x Genomics' Chromium data to further improve the scaffold NG50 (NGA50) of this assembly to 42 (15) Mbp.

Reducing Tobacco Smoke Exposure in High-Risk Infants: A Randomized, Controlled Trial.

OBJECTIVE: To evaluate a hospital-initiated intervention to reduce tobacco smoke exposure in infants in the neonatal intensive care unit. STUDY DESIGN: A randomized, controlled trial compared motivational interviewing plus financial incentives with conventional care on infant urine cotinine at 1 and 4 months' follow-up. Mothers of infants in the neonatal intensive care unit (N = 360) who reported a smoker living in the home were enrolled. Motivational interviewing sessions were delivered in both the hospital and the home. Financial incentives followed session attendance and negative infant cotinine tests postdischarge. RESULTS: The intervention effect on infant cotinine was not significant, except among mothers who reported high baseline readiness/ability to protect their infant (P ≤ .01) and mothers who completed the study within 6 months postdischarge (per protocol; P ≤ .05). Fewer mothers in the motivational interviewing plus financial incentives condition were smoking postdischarge (P ≤ .01). More mothers in the motivational interviewing plus financial incentives group reported a total home and car smoking ban at follow-up (P ≤ .05). CONCLUSIONS: Motivational interviewing combined with financial incentives reduced infant tobacco smoke exposure in a subset of women who were ready/able to protect their infant. The intervention also resulted in less maternal smoking postpartum. More robust interventions that include maternal and partner/household smoking cessation are likely needed to reduce the costly effects of tobacco smoke exposure on children and their families. TRIAL REGISTRATION: ClinicalTrials.gov: NCT01726062.

Decrease in Ambient Polycyclic Aromatic Hydrocarbon Concentrations in California's San Joaquin Valley 2000-2019.

As part of our ongoing research to understand the impact of polycyclic aromatic hydrocarbon (PAH) exposures on health in the San Joaquin Valley, we evaluated airborne PAH concentration data collected over 19 years (2000-2019) at the central air monitoring site in Fresno, California. We found a dramatic decline in outdoor airborne PAH concentrations between 2000 and 2004 that has been maintained through 2019. This decline was present in both the continuous particle-bound PAHs and the filter-based individual PAHs. The decline was more extreme when restricted to winter concentrations. Annual mean PAHs concentrations in 2017- 2018 of particle-bound PAHs were 6.8 ng/m3 or 62% lower than 2000 - 2001. The decline for winter concentrations of continuous particle-bound PAHs between winter 2019 and winter 2001 was 17.2 ng/m3, a drop of 70%. The 2001 to 2018 decline in average wintertime concentrations for filter-based individual PAHs was 82%. We examined industrial emissions, on-road vehicle emissions, residential wood burning, and agricultural and biomass waste burning as possible explanations. The major decline in PAHs from 2000-2004 was coincident with and most likely due to a similar decline in the amount of agricultural and biomass waste burned in Fresno and Madera Counties. On-road vehicle emissions and residential wood burning did not decline until after 2005. Industrial emissions were too low (2% of total) to explain such large decreases in PAH concentrations.

Prenatal exposure to air pollution, maternal diabetes and preterm birth.

Prenatal exposure to ambient air pollution has been associated with preterm birth in several studies. Associations between air pollution and gestational or pre-existing diabetes have been hypothesized but are not well established. We examined the association between air pollution exposure in pregnancy and gestational diabetes and whether the association between air pollution and preterm birth is modified by diabetes (gestational or pre-existing) in a highly polluted area of California. Birth certificates and hospital discharge data from all singleton births from 2000 to 2006 to women living in four counties in the San Joaquin Valley of California were linked to criteria air pollution and traffic density measurements at the geocoded maternal residence. Air pollutants were dichotomized at the highest quartile and compared to the lower three quartiles. Logistic regression models were adjusted for maternal race-ethnicity, age, education, payment of birth expenses, and prenatal care. There were consistent inverse associations between exposure to air pollution during the first two trimesters and gestational diabetes (statistically significant odds ratios (OR) less than 1). When stratified by any diabetes (gestational or pre-existing), associations between air pollution exposure during pregnancy and categories of preterm birth (20-27, 28-31, 32-33, 34-36 weeks) were generally similar with few exceptions of exposures to carbon monoxide (CO) and particulate matter < 2.5 µm (PM2.5). Those with diabetes and exposure higher levels of CO (in first trimester or entire pregnancy) or PM2.5 (in first trimester) had higher risk of extremely preterm birth (20-27 weeks) compared with those without diabetes. The associations between traffic-related air pollution and gestational diabetes were in the unexpected ("protective") direction. Among those with any diabetes, associations were stronger between CO and PM2.5 and extremely preterm birth.

The impact on T-regulatory cell related immune responses in rural women exposed to polycyclic aromatic hydrocarbons (PAHs) in household air pollution in Gansu, China: A pilot investigation.

Previous studies found associations between impairments of immune functions and exposure to polycyclic aromatic hydrocarbons (PAHs) in ambient air pollution in the U. S. and China. However, the results remain inconclusive due to the limitations of these studies. In this study, we aimed to examine the direction and magnitude of immune changes related to PAH exposure from household air pollution among rural women living in Gansu, China. Healthy village women (n = 34) were recruited and enrolled in the study. Questionnaires were administered. Blood and urine samples were collected and analyzed during non-heating (September 2017, "summer") and heating (January 2018, "winter") seasons. Urinary 1-hydroxypyrene (1-OHP) was quantified as the biomarker of PAH exposure. To evaluate Treg cell related immune functions, we examined immunoglobulin E (IgE), percent of T-regulatory (Treg) cells, and gene expression of following: forkhead box transcription factor 3 (Foxp3), transforming growth factor-ß (TGF-ß), interleukin 10 (IL-10), and interleukin 35 (IL-35), composed of interleukin-12 alpha (IL-12α) and Epstein-Barr-virus-induced gene 3 (EBi3). Urinary 8-hydroxy-2-deoxyguanosine (8-OHdG) was measured to evaluate oxidative DNA damage. The results showed that the concentration of 1-OHP increased from 0.90 to 17.4 µmol mol-Cr -1 from summer to winter (p < 0.001). Meanwhile, average percent of Treg cells decreased from 5.01% to 1.15% (p < 0.001); IgE and mRNA expressions of Foxp3, TGF-ß, IL-10, IL-12α and EBi3 all significantly decreased (p < 0.001); Urinary 8-OHdG increased from 12.7 to 30.3 ng mg-Cr -1 (p < 0.001). The changes in 8-OHdG, Foxp3 and TGF-ß were significantly associated with the increase of 1-OHP. The results suggested that we observed a substantial increase of PAH exposure in winter, which was significantly associated with the repression on Treg cell function and oxidative DNA damage. Exposure to PAHs in household air pollution possibly induced immune impairments among rural women in northwest China.

Incident command post exposure to polycyclic aromatic hydrocarbons and particulate matter during a wildfire.

Wildland firefighters engaged in fire suppression activities are often exposed to hazardous air pollutants such as polycyclic aromatic hydrocarbons (PAHs) and particulate matter (PM2.5) during wildfires with no respiratory protection. Although the most significant exposures to smoke likely occur on the fireline, wildland firefighters may also be exposed at the incident command post (ICP), an area designated for wildfire suppression support operations. Our objective was to characterize exposures of PAHs and PM2.5 near an ICP during a wildfire event in California. We collected area air samples for PAHs and PM2.5, during the first 12 days of a wildfire event. PAH area air samples were actively collected in 12-hr shifts (day and night) using XAD4-coated quartz fiber filters and XAD2 sorbent tubes and analyzed for 17 individual PAHs. Hourly area PM2.5 concentrations were measured with an Environmental Beta Attenuation Monitor. Most PAH concentrations generally had similar concentrations during the day and night. PM2.5 concentrations were higher during the day, due to increased fire activity, than at night. The highest concentrations of the 17 PAHs measured were for naphthalene, phenanthrene, and retene. The location of an ICP may be a critical factor in reducing these potential exposures to firefighters during wildfire events. Additionally, exposures could be reduced by utilizing clean air tents or sleeping trailers with HEPA filtration or setting up smaller camps in less smokey areas closer to the fireline for firefighters. Although measured exposures to PAHs for firefighters from smoke are lower at an ICP, these exposures still contribute to the overall cumulative work exposures.

Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes.

BACKGROUND: Alternative polyadenylation (APA) results in messenger RNA molecules with different 3' untranslated regions (3' UTRs), affecting the molecules' stability, localization, and translation. APA is pervasive and implicated in cancer. Earlier reports on APA focused on 3' UTR length modifications and commonly characterized APA events as 3' UTR shortening or lengthening. However, such characterization oversimplifies the processing of 3' ends of transcripts and fails to adequately describe the various scenarios we observe. RESULTS: We built a cloud-based targeted de novo transcript assembly and analysis pipeline that incorporates our previously developed cleavage site prediction tool, KLEAT. We applied this pipeline to elucidate the APA profiles of 114 genes in 9939 tumor and 729 tissue normal samples from The Cancer Genome Atlas (TCGA). The full set of 10,668 RNA-Seq samples from 33 cancer types has not been utilized by previous APA studies. By comparing the frequencies of predicted cleavage sites between normal and tumor sample groups, we identified 77 events (i.e. gene-cancer type pairs) of tumor-specific APA regulation in 13 cancer types; for 15 genes, such regulation is recurrent across multiple cancers. Our results also support a previous report showing the 3' UTR shortening of FGF2 in multiple cancers. However, over half of the events we identified display complex changes to 3' UTR length that resist simple classification like shortening or lengthening. CONCLUSIONS: Recurrent tumor-specific regulation of APA is widespread in cancer. However, the regulation pattern that we observed in TCGA RNA-seq data cannot be described as straightforward 3' UTR shortening or lengthening. Continued investigation into this complex, nuanced regulatory landscape will provide further insight into its role in tumor formation and development.

Kollector: transcript-informed, targeted de novo assembly of gene loci.

MOTIVATION: Despite considerable advancements in sequencing and computing technologies, de novo assembly of whole eukaryotic genomes is still a time-consuming task that requires a significant amount of computational resources and expertise. A targeted assembly approach to perform local assembly of sequences of interest remains a valuable option for some applications. This is especially true for gene-centric assemblies, whose resulting sequence can be readily utilized for more focused biological research. Here we describe Kollector, an alignment-free targeted assembly pipeline that uses thousands of transcript sequences concurrently to inform the localized assembly of corresponding gene loci. Kollector robustly reconstructs introns and novel sequences within these loci, and scales well to large genomes-properties that makes it especially useful for researchers working on non-model eukaryotic organisms. RESULTS: We demonstrate the performance of Kollector for assembling complete or near-complete Caenorhabditis elegans and Homo sapiens gene loci from their respective, input transcripts. In a time- and memory-efficient manner, the Kollector pipeline successfully reconstructs respectively 99% and 80% (compared to 86% and 73% with standard de novo assembly techniques) of C.elegans and H.sapiens transcript targets in their corresponding genomic space using whole genome shotgun sequencing reads. We also show that Kollector outperforms both established and recently released targeted assembly tools. Finally, we demonstrate three use cases for Kollector, including comparative and cancer genomics applications. AVAILABILITY AND IMPLEMENTATION: Kollector is implemented as a bash script, and is available at https://github.com/bcgsc/kollector. CONTACT: ibirol@bcgsc.ca. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Genetic variation in biotransformation enzymes, air pollution exposures, and risk of spina bifida.

Spina bifida is a birth defect characterized by incomplete closure of the embryonic neural tube. Genetic factors as well as environmental factors have been observed to influence risks for spina bifida. Few studies have investigated possible gene-environment interactions that could contribute to spina bifida risk. The aim of this study is to examine the interaction between gene variants in biotransformation enzyme pathways and ambient air pollution exposures and risk of spina bifida. We evaluated the role of air pollution exposure during pregnancy and gene variants of biotransformation enzymes from bloodspots and buccal cells in a California population-based case-control (86 cases of spina bifida and 208 non-malformed controls) study. We considered race/ethnicity and folic acid vitamin use as potential effect modifiers and adjusted for those factors and smoking. We observed gene-environment interactions between each of the five pollutants and several gene variants: NO (ABCC2), NO2 (ABCC2, SLC01B1), PM10 (ABCC2, CYP1A1, CYP2B6, CYP2C19, CYP2D6, NAT2, SLC01B1, SLC01B3), PM2.5 (CYP1A1 and CYP1A2). These analyses show positive interactions between air pollution exposure during early pregnancy and gene variants associated with metabolizing enzymes. These exploratory results suggest that some individuals based on their genetic background may be more susceptible to the adverse effects of pollution.

Personal Exposure to PM2.5 Black Carbon and Aerosol Oxidative Potential using an Automated Microenvironmental Aerosol Sampler (AMAS).

Traditional methods for measuring personal exposure to fine particulate matter (PM2.5) are cumbersome and lack spatiotemporal resolution; methods that are time-resolved are limited to a single species/component of PM. To address these limitations, we developed an automated microenvironmental aerosol sampler (AMAS), capable of resolving personal exposure by microenvironment. The AMAS is a wearable device that uses a GPS sensor algorithm in conjunction with a custom valve manifold to sample PM2.5 onto distinct filter channels to evaluate home, school, and other (e.g., outdoors, in transit, etc.) exposures. Pilot testing was conducted in Fresno, CA where 25 high-school participants ( n = 37 sampling events) wore an AMAS for 48-h periods in November 2016. Data from 20 (54%) of the 48-h samples collected by participants were deemed valid and the filters were analyzed for PM2.5 black carbon (BC) using light transmissometry and aerosol oxidative potential (OP) using the dithiothreitol (DTT) assay. The amount of inhaled PM2.5 was calculated for each microenvironment to evaluate the health risks associated with exposure. On average, the estimated amount of inhaled PM2.5 BC (µg day-1) and OP [(µM min-1) day-1] was greatest at home, owing to the proportion of time spent within that microenvironment. Validation of the AMAS demonstrated good relative precision (8.7% among collocated instruments) and a mean absolute error of 22% for BC and 33% for OP when compared to a traditional personal sampling instrument. This work demonstrates the feasibility of new technology designed to quantify personal exposure to PM2.5 species within distinct microenvironments.

Occupational Exposure to Polycyclic Aromatic Hydrocarbon of Wildland Firefighters at Prescribed and Wildland Fires.

Wildland firefighters suppressing wildland fires or conducting prescribed fires work long shifts during which they are exposed to high levels of wood smoke with no respiratory protection. Polycyclic aromatic hydrocarbons (PAHs) are hazardous air pollutants formed during incomplete combustion. Exposure to PAHs was measured for 21 wildland firefighters suppressing two wildland fires and 4 wildland firefighters conducting prescribed burns in California. Personal air samples were actively collected using XAD4-coated quartz fiber filters and XAD2 sorbent tubes. Samples were analyzed for 17 individual PAHs through extraction with dichloromethane and gas chromatograph-mass spectrometer analysis. Naphthalene, retene, and phenanthrene were consistently the highest measured PAHs. PAH concentrations were higher at wildland fires compared to prescribed fires and were highest for firefighters during job tasks that involve the most direct contact with smoke near an actively burning wildland fire. Although concentrations did not exceed current occupational exposure limits, wildland firefighters are exposed to PAHs not only on the fire line at wildland fires, but also while working prescribed burns and while off-duty. Characterization of occupational exposures from wildland firefighting is important to understand better any potential long-term health effects.

A task-based assessment of parental occupational exposure to pesticides and childhood acute lymphoblastic leukemia.

OBJECTIVES: Associations between parental occupational pesticide exposure and childhood acute lymphoblastic leukemia (ALL) vary across studies, likely due to different exposure assessment methodologies. METHODS: We assessed parental occupational pesticide exposure from the year before pregnancy to the child's third year of life for 669 children diagnosed with ALL and 1021 controls. We conducted expert rating using task-based job modules (JM) to estimate exposure to pesticides among farmer workers, gardeners, agricultural packers, and pesticide applicators. We compared this method to (1) partial JM using job titles and a brief description, but without completing the task-based questionnaire, and (2) job exposure matrix (JEM) linking job titles to the International Standard Classifications of Occupation Codes. We used unconditional logistic regression to calculate odds ratios (OR) and 95% confidence intervals (95% CI) for ALL cancer risk and pesticide exposure adjusting for child's sex, age, race/ethnicity and household income. RESULTS: Compared to complete JMs, partial JMs and JEM led to 3.1% and 9.4% of parents with pesticide exposure misclassified, respectively. Misclassification was similar in cases and controls. Using complete JMs, we observed an increased risk of ALL for paternal occupational exposure to any pesticides (OR=1.7; 95% CI=1.2, 2.5), with higher risks reported for pesticides to treat nut crops (OR=4.5; 95% CI=0.9, 23.0), and for children diagnosed before five years of age (OR=2.3; 95% CI: 1.3, 4.1). Exposure misclassification from JEM attenuated these associations by about 57%. Maternal occupational pesticide exposure before and after birth was not associated with ALL. CONCLUSIONS: The risk of ALL was elevated in young children with paternal occupational pesticide exposure during the perinatal period, using more detailed occupational information for exposure classification.

Acquired Color Vision Defects and Hexane Exposure: A Study of San Francisco Bay Area Automotive Mechanics.

Occupational exposure to solvents, including n-hexane, has been associated with acquired color vision defects. Blue-yellow defects are most common and may be due to neurotoxicity or retinal damage. Acetone may potentiate the neurotoxicity of n-hexane. We present results on nonhexane solvent and hexane exposure and color vision from a cross-sectional study of 835 automotive repair workers in the San Francisco Bay Area, California (2007-2013). Cumulative exposure was estimated from self-reported work history, and color vision was assessed using the Lanthony desaturated D-15 panel test. Log-binomial regression was used to estimate prevalence ratios for color vision defects. Acquired color vision defects were present in 29% of participants, of which 70% were blue-yellow. Elevated prevalence ratios were found for nonhexane solvent exposure, with a maximum of 1.31 (95% confidence interval (CI): 0.86, 2.00) for blue-yellow. Among participants aged ≤50 years, the prevalence ratio for blue-yellow defects was 2.17 (95% CI: 1.03, 4.56) in the highest quartile of nonhexane solvent exposure and 1.62 (95% CI: 0.97, 2.72) in the highest category of exposure to hexane with acetone coexposure. Cumulative exposures to hexane and nonhexane solvents in the highest exposure categories were associated with elevated prevalence ratios for color vision defects in younger participants.